TrakEM2 - How to select all patches that are linked to each other across layers?


This seems painfully simple but I can’t figure out how to do it for the life of me. I have a 700 layer stack of 1x3 tiled EM images open in TrakEM2. I want to move all of the 700 images belonging to one of the tiles up so they overlap their neighbor, but I cant figure out how to make a selection on all of the images in the stack. I don’t want to do it layer by layer for obvious reasons. Any advice?


Hi @connont,

Welcome to the forum!

I would do it with:
right click > Selection > Select all that match...
And then you can chose your starting and ending layers to include in the selection (all layers, in your case).

You can match certain tiles by giving a regular expression. This depends on your tiles being named in such a way that they’re differentiated from each other (i.e., if everything is named the same, it won’t help).

Hope this helps,

Hi John,

Thanks for your response! I thought a solution might involve that…unfortunately, the imaging software I use saves them only with slice information, i.e. there is nothing differentiating them by tile.

Do you think that is the only solution? I suppose I will need to rename all the files and reload them to have the ability to select a specific stack…

Thanks :slight_smile:


How did you import the tiles into TrakEM2?
Are all the tiles in a stack the same size and directly “on top” of one another?



Three folders containing all the images were dragged into the project and manually aligned.
The tiles belonging to one stack are all the same size, but they are not quite directly on top of one another (they were automatically aligned).